Difference between revisions of "2012 GOC Meeting Caltech"

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[[Category:GO Consortium Meetings]]
 
= [[2012 Caltech GOC Meeting Logistics]] =
 
= [[2012 Caltech GOC Meeting Logistics]] =
 
Follow Link to [https://docs.google.com/document/d/1h85nGcAFs2qzhslpuxDpj06V1y84GwVJ7l2TJA_PmSE/edit meeting minutes as a Google Doc]
 
Follow Link to [https://docs.google.com/document/d/1h85nGcAFs2qzhslpuxDpj06V1y84GwVJ7l2TJA_PmSE/edit meeting minutes as a Google Doc]
<p>
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Today's wireless:
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* name: NETGEAR49(-5G)
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* pass: rockyrabbit990
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MONDAY:  Millikin Library; coffee at 0830; snack at 1500; lunch on your own (Chandler Cafeteria)
 
MONDAY:  Millikin Library; coffee at 0830; snack at 1500; lunch on your own (Chandler Cafeteria)
  
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** WormBase experience with protein2go (Kimberly)
 
** WormBase experience with protein2go (Kimberly)
 
** Wormbase CC tool (Kimberly)
 
** Wormbase CC tool (Kimberly)
** Migration plans (Suzi)
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** Migration plans (Suzi) [[File: p2go transition.pdf]]
 
*** Short term: towards protein2go
 
*** Short term: towards protein2go
 
*** Longer term: capabilities to support LEGO
 
*** Longer term: capabilities to support LEGO
 
* Enrichment (and other) tool improvement plans (Chris)
 
* Enrichment (and other) tool improvement plans (Chris)
** Standardize interface to tools & allow plug in play eg via [[Galaxy]]
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** Standardize interface to tools & allow plug in play eg via [[Galaxy]] [http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/meeting/consortium/Pasadena2012/GO-Galaxy.pptx pptx]
 
** Promote tools that provide access to latest GO, work with those that don't. See [[GO Tools Registry]]
 
** Promote tools that provide access to latest GO, work with those that don't. See [[GO Tools Registry]]
 
** Getting enrichment tools to leverage ontology and annotation improvements
 
** Getting enrichment tools to leverage ontology and annotation improvements
 
* PAINT (Paul T)
 
* PAINT (Paul T)
 
** SwissProt strategy for protein family annotation (Alan)
 
** SwissProt strategy for protein family annotation (Alan)
** PAINT user guide (Huaiyu)
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** PAINT user guide (Huaiyu) at http://wiki.geneontology.org/index.php/PAINT_User_Guide
 
** PAINT annotation progress
 
** PAINT annotation progress
  
 
= Annotation Production - Judy Tuesday morning=
 
= Annotation Production - Judy Tuesday morning=
* Annotation Production Progress/Tracking (Paul S)
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==Annotation==
** volume of annotations
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* Annotation Measurement of Success(Mike)
** backlog of papers selected
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** [[File:GO-annotations.201201008-2.pdf | Measures 2012]]
** New reporting page
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** "Quality" aka Reproducibility
** Observations/Comments
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* Annotation Hard Checks. (Mike)
* Term requests (Judy/Jane)
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** Have removed IEAs from JCVI, Gramene, GeneDB P. falciparum, GeneDB tsetse, Pseudocap because > 2yr out of date
** Current rate of additions & rate of clearance
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** Propose to remove IEAs from CGD, AspDB, GeneDB L. major, GeneDB T. brucei, and include up to date IEAs from GOA
 +
*** General rule: this will be done for any other projects that *DO NOT* include annotations from GOA.
 +
** We filter out IEA annotations that are older than 1 year.  Should we be filtering out ISS say after 2 years?
 
* Standard processing of uploaded annotations
 
* Standard processing of uploaded annotations
 
** [http://www.geneontology.org/GO.annotation_qc.shtml Automated annotation QC] (Chris/Heiko ~5 slides + demo) [[File:GOC-Meeting-2012-Oct-Automated_QC_for_annotations.pdf]]
 
** [http://www.geneontology.org/GO.annotation_qc.shtml Automated annotation QC] (Chris/Heiko ~5 slides + demo) [[File:GOC-Meeting-2012-Oct-Automated_QC_for_annotations.pdf]]
** Annotation "Quality", Reproducibility, measures (Mike)
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* Redundant/non-redundant annotations (Rama) [[File:RedundantCaltech2012.pdf‎]]
** Filtering of taxid that are not supported. (Mike)
 
*** Have removed JCVI, Gramene, GeneDB P. falciparum, GeneDB tsetse, Pseudocap
 
*** Propose to remove CGD, AspDB, GeneDB L. major, GeneDB T. brucei, and any other projects that *DO NOT* include annotations from GOA.
 
*** We filter out IEA annotations that are older than 1 year.  Should we be filtering out ISS say after 2 years?
 
* Redundant/non-redundant annotations (Rama will summarize what was discussed during Annotation Calls)  
 
 
* Provenance of evidence (Rama)
 
* Provenance of evidence (Rama)
* Current ontology development and annotation topics on the table (one slide each, Judy to present)
 
** cardio conduction (Ruth)
 
** apoptosis (Paola)
 
** cell cycle (Val or Judy)
 
** tRNA Modification (Harold)
 
** review of approach, staging (Judy)
 
* Ontology development workflow and coordination (Paul and Judy)
 
* BioCreative Challenge IV - GO Triage and Annotation (Kimberly, James, Donghui, Judy)
 
 
* Submissions and outreach to outside groups
 
* Submissions and outreach to outside groups
 
** Web page with instructions (Rama)
 
** Web page with instructions (Rama)
 
** Pulling in external annotations
 
** Pulling in external annotations
** Future work - who has been in contact? any active outreach?
 
  
= Set objectives for next period (Paul S) Tuesday late afternoon =
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==Annotation via Ontology: Production and Priorities==
* Strategy for prioritization of ontology development topics (Paul S and Paul)
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[[File:OverviewOntologyAnnotation.pdf]]
** Emily summation of needed areas aka textbook
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* Current ontology development and annotation topics on the table
** Information content approach
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** ONE: Term requests (Jane)
 +
***Current rate of additions & rate of clearance
 +
** TWO: topic oriented via community interest
 +
*** cardio conduction (Ruth)
 +
*** apoptosis (Paola)
 +
*** cell cycle (Val)
 +
*** tRNA Modification (Harold)
 +
** THREE global review of coverage
 +
* Priority of Ontology development workflow and coordination
 +
** Strategy for prioritization of ontology development topics
 +
*** Emily summation of needed areas aka textbook
 +
*** Information content approac
 +
 
 +
= Wrap-Up (Paul S) Tuesday 1140 =
 +
* Review Action Items
 +
* Set objectives for next period
 +
* Discuss / decide on tag for Logo competition
 +
* Wrap-up
 +
* Group Photos
 +
[[File:GOC Caltech-1..JPG|200px|thumb|left|Photo 1]] [[File:GOC-Caltech-2.JPG|200px|thumb|center|Photo 2]]

Latest revision as of 09:25, 8 April 2014

2012 Caltech GOC Meeting Logistics

Follow Link to meeting minutes as a Google Doc

Today's wireless:

  • name: NETGEAR49(-5G)
  • pass: rockyrabbit990

MONDAY: Millikin Library; coffee at 0830; snack at 1500; lunch on your own (Chandler Cafeteria)

Biological relevance - Paul S - Sunday 10:30

024 Beckman Behavioral Biology Building; [coffee at 09:30; lunch 1at 1230]

Web - Cherry - Sunday afternoon

Biological Representation - Paul T - Sunday aft - Monday morning

  • Management of Ontology Development
  • Incorporation of External ontologies (David and Jane)
    • CHEBI (David) File:Chemicals Caltech.pdf done Sunday afternoon
    • Report on migration of NIF subcellular AO to GO-CC (Jane)
    • Rhea - importing enzymatic reactions (Jane)
    • BFO 2.0 - (Chris)
      • do we comply with BFO and split part_of into 2 relations? Need 'official' signoff of GO's stance
  • Extensions to the GO annotation model
    • LEGO data model, an 'annoton' (Chris and Paul) pptx
      • For prototyping: Protege plug-in for annotation (Heiko)
      • Current examples (Kimberly and David)
    • col. 16 extensions (Paul, Chris, Jane, Rachael)
      • GPAD releases
      • relationship to LEGO

Project infrastructure - Suzi - Monday afternoon

  • CAT
    • Architecture, services (Suzi) File:CAT-webservices.pdf
    • protein2go introduction (Rachael)
    • WormBase experience with protein2go (Kimberly)
    • Wormbase CC tool (Kimberly)
    • Migration plans (Suzi) File:P2go transition.pdf
      • Short term: towards protein2go
      • Longer term: capabilities to support LEGO
  • Enrichment (and other) tool improvement plans (Chris)
    • Standardize interface to tools & allow plug in play eg via Galaxy pptx
    • Promote tools that provide access to latest GO, work with those that don't. See GO Tools Registry
    • Getting enrichment tools to leverage ontology and annotation improvements
  • PAINT (Paul T)

Annotation Production - Judy Tuesday morning

Annotation

  • Annotation Measurement of Success(Mike)
  • Annotation Hard Checks. (Mike)
    • Have removed IEAs from JCVI, Gramene, GeneDB P. falciparum, GeneDB tsetse, Pseudocap because > 2yr out of date
    • Propose to remove IEAs from CGD, AspDB, GeneDB L. major, GeneDB T. brucei, and include up to date IEAs from GOA
      • General rule: this will be done for any other projects that *DO NOT* include annotations from GOA.
    • We filter out IEA annotations that are older than 1 year. Should we be filtering out ISS say after 2 years?
  • Standard processing of uploaded annotations
  • Redundant/non-redundant annotations (Rama) File:RedundantCaltech2012.pdf
  • Provenance of evidence (Rama)
  • Submissions and outreach to outside groups
    • Web page with instructions (Rama)
    • Pulling in external annotations

Annotation via Ontology: Production and Priorities

File:OverviewOntologyAnnotation.pdf

  • Current ontology development and annotation topics on the table
    • ONE: Term requests (Jane)
      • Current rate of additions & rate of clearance
    • TWO: topic oriented via community interest
      • cardio conduction (Ruth)
      • apoptosis (Paola)
      • cell cycle (Val)
      • tRNA Modification (Harold)
    • THREE global review of coverage
  • Priority of Ontology development workflow and coordination
    • Strategy for prioritization of ontology development topics
      • Emily summation of needed areas aka textbook
      • Information content approac

Wrap-Up (Paul S) Tuesday 1140

  • Review Action Items
  • Set objectives for next period
  • Discuss / decide on tag for Logo competition
  • Wrap-up
  • Group Photos
Photo 1
Photo 2